On Thu, Nov 22, 2012 at 2:50 AM, Gustavo Fern?ndez Bay?n <gbayon at="" gmail.com=""> wrote: > > Hi Kasper. > > It's perfectly clear for me now what rs* probes are. I should have read the Illumina guide before, I guess. But it is always a pleasure to ask in this list and learn a little bit more. > > I agree with your decision about removing the probes. Problem is, GenomeStudio is calculating the betas for those probes too, which is something I think can lead to confusion. In my humble opinion, if something is not measuring methylation, showing a beta value for it on your interface is going to make a new user go mad (as has effectively happened to a fellow biologist in my lab). Glad that we agree. If you (or anyone else) have an awesome application for the rs probes, feel free to tell us. > I have another question. I was wondering about opening a new topic, but I think it might fit in this context. Why is minfi not using the correction constant 100 in the denominator when calculating the betas? I have always wondered about that constant, because I did not see the exact reasoning behind it, and I am inclined to think more in your way o implementing it. In the end, it really makes no difference, doesn't it? Well, they are trying to avoid a divide by zero problem. Whether or not that is important to handle also depends on how the data was normalized. It is easy to imagine a normalization procedure that makes sure that this never happens (for example a procedure that bounds all probe intensities away from zero). For such a normalization procedure, adding 100 makes little sense. In our implementation, you can choose to add a 100, but that default is zero. For most probes this should make no difference, but there may be a few where it matters. Kasper > Regards, > Gus > > --------------------------- > Enviado con Sparrow (http://www.sparrowmailapp.com/?sig) > > > El mi?rcoles 21 de noviembre de 2012 a las 17:35, Kasper Daniel Hansen escribi?: > >> The 'rs' probes are normal SNP probes; they do not measure >> methylation. Quoting from the Illumina methylation guide >> "rs# representsSNPassays (not affected by DNA methylation)" >> and >> "SNP assays can be used for sample identification and tracking. They >> >> should be excluded for differential methylation analysis." > >> >> The purpose of these probes is for catching sample mix-ups. We have >> decided to remove them from the methylation object (MethylSet) because >> they do not measure methylation and the purpose of this object is to >> contain the methylation measurements. >> >> Kasper >> >> >> >> >> On Wed, Nov 21, 2012 at 4:38 AM, Gustavo Fern?ndez Bay?n >> <gbayon at="" gmail.com="" (mailto:gbayon="" at="" gmail.com)=""> wrote: >> > Hi everybody. >> > >> > I have just noticed that some probes disappeared during my workflow with minfi. When I looked into the preprocessing, I saw that preprocessIllumina() ends up calling preprocessRaw() in order to generate M and U signals. The interesting part is, only probes of type I and II are used for that. I noticed that the probes that were disappearing in my workflow are of type 'SNPI' and 'SNPII'. >> > >> > Now I know in which part the probes are lost, but I would like to know the reason behind this procedure. Also, could anybody give me a hint if this is what Genomestudio is doing? What are this rs* probes useful for then? >> > >> > Regards, >> > Gus >> > >> > >> > >> > --------------------------- >> > Enviado con Sparrow (http://www.sparrowmailapp.com/?sig) >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org (mailto:Bioconductor at r-project.org) >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > >